Long Noncoding RNA Lncshgl Recruits Hnrnpa1 to Suppress Hepatic Gluconeogenesis and Lipogenesis
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Lineage-Specific Evolution of the Vertebrate Otopetrin Gene Family Revealed by Comparative Genomic Analyses
Hurle et al. BMC Evolutionary Biology 2011, 11:23 http://www.biomedcentral.com/1471-2148/11/23 RESEARCHARTICLE Open Access Lineage-specific evolution of the vertebrate Otopetrin gene family revealed by comparative genomic analyses Belen Hurle1, Tomas Marques-Bonet2,3, Francesca Antonacci3, Inna Hughes4, Joseph F Ryan1, NISC Comparative Sequencing Program1,5, Evan E Eichler3, David M Ornitz6, Eric D Green1,5* Abstract Background: Mutations in the Otopetrin 1 gene (Otop1) in mice and fish produce an unusual bilateral vestibular pathology that involves the absence of otoconia without hearing impairment. The encoded protein, Otop1, is the only functionally characterized member of the Otopetrin Domain Protein (ODP) family; the extended sequence and structural preservation of ODP proteins in metazoans suggest a conserved functional role. Here, we use the tools of sequence- and cytogenetic-based comparative genomics to study the Otop1 and the Otop2-Otop3 genes and to establish their genomic context in 25 vertebrates. We extend our evolutionary study to include the gene mutated in Usher syndrome (USH) subtype 1G (Ush1g), both because of the head-to-tail clustering of Ush1g with Otop2 and because Otop1 and Ush1g mutations result in inner ear phenotypes. Results: We established that OTOP1 is the boundary gene of an inversion polymorphism on human chromosome 4p16 that originated in the common human-chimpanzee lineage more than 6 million years ago. Other lineage- specific evolutionary events included a three-fold expansion of the Otop genes in Xenopus tropicalis and of Ush1g in teleostei fish. The tight physical linkage between Otop2 and Ush1g is conserved in all vertebrates. -
Gateways to the FANTOM5 Promoter Level Mammalian Expression Atlas
Lizio et al. Genome Biology (2015) 16:22 DOI 10.1186/s13059-014-0560-6 SOFTWARE Open Access Gateways to the FANTOM5 promoter level mammalian expression atlas Marina Lizio1,2, Jayson Harshbarger1,2, Hisashi Shimoji1,2, Jessica Severin1,2, Takeya Kasukawa2, Serkan Sahin1,2, Imad Abugessaisa2, Shiro Fukuda1, Fumi Hori1,2, Sachi Ishikawa-Kato1,2, Christopher J Mungall5, Erik Arner1,2, J Kenneth Baillie7, Nicolas Bertin1,2,19, Hidemasa Bono10, Michiel de Hoon1,2, Alexander D Diehl13, Emmanuel Dimont12, Tom C Freeman7, Kaori Fujieda10, Winston Hide12,17, Rajaram Kaliyaperumal8, Toshiaki Katayama15, Timo Lassmann1,2,18, Terrence F Meehan6, Koro Nishikata16, Hiromasa Ono10, Michael Rehli9, Albin Sandelin11, Erik A Schultes8,14, Peter AC ‘t Hoen8, Zuotian Tatum8, Mark Thompson8, Tetsuro Toyoda16, Derek W Wright7, Carsten O Daub1, Masayoshi Itoh1,2,3, Piero Carninci1,2, Yoshihide Hayashizaki1,3, Alistair RR Forrest1,2*, Hideya Kawaji1,2,3,4* and the FANTOM consortium Abstract The FANTOM5 project investigates transcription initiation activities in more than 1,000 human and mouse primary cells, cell lines and tissues using CAGE. Based on manual curation of sample information and development of an ontology for sample classification, we assemble the resulting data into a centralized data resource (http://fantom. gsc.riken.jp/5/). This resource contains web-based tools and data-access points for the research community to search and extract data related to samples, genes, promoter activities, transcription factors and enhancers across the FANTOM5 atlas. Introduction ontologies [10]). However, the ability of these surveys to One of the most comprehensive ways to study the mo- quantify RNA abundance was limited mainly due to se- lecular basis of cellular function is to quantify the pres- quencing performance. -
743914V1.Full.Pdf
bioRxiv preprint doi: https://doi.org/10.1101/743914; this version posted August 24, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 1 Cross-talks of glycosylphosphatidylinositol biosynthesis with glycosphingolipid biosynthesis 2 and ER-associated degradation 3 4 Yicheng Wang1,2, Yusuke Maeda1, Yishi Liu3, Yoko Takada2, Akinori Ninomiya1, Tetsuya 5 Hirata1,2,4, Morihisa Fujita3, Yoshiko Murakami1,2, Taroh Kinoshita1,2,* 6 7 1Research Institute for Microbial Diseases, Osaka University, Suita, Osaka 565-0871, Japan 8 2WPI Immunology Frontier Research Center, Osaka University, Suita, Osaka 565-0871, 9 Japan 10 3Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, 11 School of Biotechnology, Jiangnan University, Wuxi, Jiangsu 214122, China 12 4Current address: Center for Highly Advanced Integration of Nano and Life Sciences (G- 13 CHAIN), Gifu University, 1-1 Yanagido, Gifu-City, Gifu 501-1193, Japan 14 15 *Correspondence and requests for materials should be addressed to T.K. (email: 16 [email protected]) 17 18 19 Glycosylphosphatidylinositol (GPI)-anchored proteins and glycosphingolipids interact with 20 each other in the mammalian plasma membranes, forming dynamic microdomains. How their 21 interaction starts in the cells has been unclear. Here, based on a genome-wide CRISPR-Cas9 22 genetic screen for genes required for GPI side-chain modification by galactose in the Golgi 23 apparatus, we report that b1,3-galactosyltransferase 4 (B3GALT4), also called GM1 24 ganglioside synthase, additionally functions in transferring galactose to the N- 25 acetylgalactosamine side-chain of GPI. -
Evaluation of Variability in Human Protein X-Ray Structures Risa Anzai
bioRxiv preprint doi: https://doi.org/10.1101/202028; this version posted October 12, 2017. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. Evaluation of variability in human protein X-ray structures Risa Anzai, Yoshiki Asami, Waka Inoue, Hina Ueno, Koya Yamada, Tetsuji Okada Department of Life Science, Gakushuin University, 1-5-1 Mejiro, Toshima-ku, Tokyo 171-8588, Japan. Corresponding author: Tetsuji Okada, Department of Life Science, Gakushuin University, 1-5-1 Mejiro, Toshima-ku, Tokyo 171-8588, Japan. +81-3-3986-0221, [email protected] Abstract Systematic analysis of statistical and dynamical properties of proteins is critical to understanding cellular events. Extraction of biologically relevant information from a set of X-ray structures is important because it can provide mechanistic details behind the functional properties of protein families, enabling rational comparison between families. Most of the current structure comparisons are pairwise-based, which hampers the global analysis of increasing contents in the Protein Data Bank. Additionally, pairing of protein structures introduces uncertainty with respect to reproducibility because it frequently accompanies other settings such as alignment and/or superimposition. This study introduces intramolecular distance scoring, for the analysis of human proteins, for each of which at least several X-ray structures are available. We show that the results are comprehensively used to overview advances at the atomic level exploration of each protein and protein family. -
Relevance Network Between Chemosensitivity and Transcriptome in Human Hepatoma Cells1
Vol. 2, 199–205, February 2003 Molecular Cancer Therapeutics 199 Relevance Network between Chemosensitivity and Transcriptome in Human Hepatoma Cells1 Masaru Moriyama,2 Yujin Hoshida, topoisomerase II  expression, whereas it negatively Motoyuki Otsuka, ShinIchiro Nishimura, Naoya Kato, correlated with expression of carboxypeptidases A3 Tadashi Goto, Hiroyoshi Taniguchi, and Z. Response to nimustine was associated with Yasushi Shiratori, Naohiko Seki, and Masao Omata expression of superoxide dismutase 2. Department of Gastroenterology, Graduate School of Medicine, Relevance networks identified several negative University of Tokyo, Tokyo 113-8655 [M. M., Y. H., M. O., N. K., T. G., H. T., Y. S., M. O.]; Cellular Informatics Team, Computational Biology correlations between gene expression and resistance, Research Center, Tokyo 135-0064 [S. N.]; and Department of which were missed by hierarchical clustering. Our Functional Genomics, Graduate School of Medicine, Chiba University, results suggested the necessity of systematically Chiba 260-8670 [N. S.], Japan evaluating the transporting systems that may play a major role in resistance in hepatoma. This may provide Abstract useful information to modify anticancer drug action in Generally, hepatoma is not a chemosensitive tumor, hepatoma. and the mechanism of resistance to anticancer drugs is not fully elucidated. We aimed to comprehensively Introduction evaluate the relationship between chemosensitivity and Hepatoma is a major cause of death even in developed gene expression profile in human hepatoma cells, by countries, and its incidence is increasing (1). Despite the using microarray analysis, and analyze the data by progress of therapeutic technique (2), the efficacy of radical constructing relevance networks. therapy is hampered by frequent recurrence and advance of In eight hepatoma cell lines (HLE, HLF, Huh7, Hep3B, the tumor (3). -
Multiplexed Engineering Glycosyltransferase Genes in CHO Cells Via Targeted Integration for Producing Antibodies with Diverse Complex‑Type N‑Glycans Ngan T
www.nature.com/scientificreports OPEN Multiplexed engineering glycosyltransferase genes in CHO cells via targeted integration for producing antibodies with diverse complex‑type N‑glycans Ngan T. B. Nguyen, Jianer Lin, Shi Jie Tay, Mariati, Jessna Yeo, Terry Nguyen‑Khuong & Yuansheng Yang* Therapeutic antibodies are decorated with complex‑type N‑glycans that signifcantly afect their biodistribution and bioactivity. The N‑glycan structures on antibodies are incompletely processed in wild‑type CHO cells due to their limited glycosylation capacity. To improve N‑glycan processing, glycosyltransferase genes have been traditionally overexpressed in CHO cells to engineer the cellular N‑glycosylation pathway by using random integration, which is often associated with large clonal variations in gene expression levels. In order to minimize the clonal variations, we used recombinase‑mediated‑cassette‑exchange (RMCE) technology to overexpress a panel of 42 human glycosyltransferase genes to screen their impact on antibody N‑linked glycosylation. The bottlenecks in the N‑glycosylation pathway were identifed and then released by overexpressing single or multiple critical genes. Overexpressing B4GalT1 gene alone in the CHO cells produced antibodies with more than 80% galactosylated bi‑antennary N‑glycans. Combinatorial overexpression of B4GalT1 and ST6Gal1 produced antibodies containing more than 70% sialylated bi‑antennary N‑glycans. In addition, antibodies with various tri‑antennary N‑glycans were obtained for the frst time by overexpressing MGAT5 alone or in combination with B4GalT1 and ST6Gal1. The various N‑glycan structures and the method for producing them in this work provide opportunities to study the glycan structure‑and‑function and develop novel recombinant antibodies for addressing diferent therapeutic applications. -
Long Non-Coding RNA Lncshgl Recruits Hnrnpa1 to Suppress Hepatic Gluconeogenesis and Lipogenesis
Page 1 of 60 Diabetes Long non-coding RNA LncSHGL recruits hnRNPA1 to suppress hepatic gluconeogenesis and lipogenesis Junpei Wang1,2#, Weili Yang1,2#, Zhenzhen Chen1, Ji Chen1, Yuhong Meng1, Biaoqi Feng1, Libo Sun3, Lin Dou4, Jian Li4, Qinghua Cui2*, Jichun Yang1* 1Department of Physiology and Pathophysiology, School of Basic Medical Sciences Key Laboratory of Molecular Cardiovascular Sciences of the Ministry of Education Center for Non-coding RNA Medicine Peking University Health Science Center Beijing 100191, China 2Department of Biomedical Informatics, School of Basic Medical Sciences Key Laboratory of Molecular Cardiovascular Sciences of the Ministry of Education, Center for Non-coding RNA Medicine Peking University Health Science Center, Beijing 100191, China 3Beijing You An Hospital,Capital Medical University, Beijing 100069, China 4Key Laboratory of Geriatrics, Beijing Institute of Geriatrics & Beijing Hospital, Ministry of Health, Beijing 100730, China #These authors contributed equally to this work *Correspondence to: Jichun Yang, Ph.D. Department of Physiology and Pathophysiology, School of Basic Medical Sciences Peking University Health Science Center, Beijing 100191, China Email: [email protected]; Tel: (+86) 10-82801403 Or to: Qinghua Cui, Ph.D. Department of Biomedical Informatics, School of Basic Medical Sciences Peking University Health Science Center, Beijing 100191, China Email:[email protected]; Tel:(+86)10-82801585 1 Diabetes Publish Ahead of Print, published online January 30, 2018 Diabetes Page 2 of 60 Abstract Mammalian genomes encode a huge number of LncRNAs with unknown functions. This study determined the role and mechanism of a new LncRNA, LncRNA Suppressor of Hepatic Gluconeogenesis and Lipogenesis (LncSHGL), in regulating hepatic glucose/lipid metabolism. -
Role and Regulation of the P53-Homolog P73 in the Transformation of Normal Human Fibroblasts
Role and regulation of the p53-homolog p73 in the transformation of normal human fibroblasts Dissertation zur Erlangung des naturwissenschaftlichen Doktorgrades der Bayerischen Julius-Maximilians-Universität Würzburg vorgelegt von Lars Hofmann aus Aschaffenburg Würzburg 2007 Eingereicht am Mitglieder der Promotionskommission: Vorsitzender: Prof. Dr. Dr. Martin J. Müller Gutachter: Prof. Dr. Michael P. Schön Gutachter : Prof. Dr. Georg Krohne Tag des Promotionskolloquiums: Doktorurkunde ausgehändigt am Erklärung Hiermit erkläre ich, dass ich die vorliegende Arbeit selbständig angefertigt und keine anderen als die angegebenen Hilfsmittel und Quellen verwendet habe. Diese Arbeit wurde weder in gleicher noch in ähnlicher Form in einem anderen Prüfungsverfahren vorgelegt. Ich habe früher, außer den mit dem Zulassungsgesuch urkundlichen Graden, keine weiteren akademischen Grade erworben und zu erwerben gesucht. Würzburg, Lars Hofmann Content SUMMARY ................................................................................................................ IV ZUSAMMENFASSUNG ............................................................................................. V 1. INTRODUCTION ................................................................................................. 1 1.1. Molecular basics of cancer .......................................................................................... 1 1.2. Early research on tumorigenesis ................................................................................. 3 1.3. Developing -
Suppression of the Peripheral Immune System Limits the Central Immune Response Following Cuprizone-Feeding: Relevance to Modelling Multiple Sclerosis
cells Article Suppression of the Peripheral Immune System Limits the Central Immune Response Following Cuprizone-Feeding: Relevance to Modelling Multiple Sclerosis Monokesh K. Sen 1 , Mohammed S. M. Almuslehi 1,2, Erika Gyengesi 1, Simon J. Myers 3, Peter J. Shortland 3, David A. Mahns 1,* and Jens R. Coorssen 4,* 1 School of Medicine, Western Sydney University, Locked Bag 1797, Penrith, NSW 2751, Australia; [email protected] (M.K.S.); [email protected] (M.S.M.A.); [email protected] (E.G.) 2 Department of Physiology, College of Veterinary Medicine, Diyala University, Diyala, Iraq 3 School of Science and Health, Western Sydney University, Locked Bag 1797, Penrith, NSW 2751, Australia; [email protected] (S.J.M.); [email protected] (P.J.S.) 4 Department of Health Sciences, Faculty of Applied Health Sciences, and Department of Biological Sciences, Faculty of Mathematics and Science, Brock University, St. Catharines, Ontario, ON L2S 3A1, Canada * Correspondence: [email protected] (D.A.M.); [email protected] (J.R.C.); Tel.: +02-4620-3784 (D.A.M.); +905-688-5550 (J.R.C.) Received: 6 September 2019; Accepted: 18 October 2019; Published: 24 October 2019 Abstract: Cuprizone (CPZ) preferentially affects oligodendrocytes (OLG), resulting in demyelination. To investigate whether central oligodendrocytosis and gliosis triggered an adaptive immune response, the impact of combining a standard (0.2%) or low (0.1%) dose of ingested CPZ with disruption of the blood brain barrier (BBB), using pertussis toxin (PT), was assessed in mice. 0.2% CPZ( PT) for ± 5 weeks produced oligodendrocytosis, demyelination and gliosis plus marked splenic atrophy (37%) and reduced levels of CD4 (44%) and CD8 (61%). -
This Article Appeared in a Journal Published by Elsevier. the Attached
This article appeared in a journal published by Elsevier. The attached copy is furnished to the author for internal non-commercial research and education use, including for instruction at the authors institution and sharing with colleagues. Other uses, including reproduction and distribution, or selling or licensing copies, or posting to personal, institutional or third party websites are prohibited. In most cases authors are permitted to post their version of the article (e.g. in Word or Tex form) to their personal website or institutional repository. Authors requiring further information regarding Elsevier’s archiving and manuscript policies are encouraged to visit: http://www.elsevier.com/copyright Author's personal copy Livestock Science 131 (2010) 297–300 Contents lists available at ScienceDirect Livestock Science journal homepage: www.elsevier.com/locate/livsci Short communication Polymorphisms of the β-1,4 galactosyltransferase-I gene in Holsteins Homayon Reza Shahbazkia a,⁎, Mahmoud Aminlari b, Atoosa Tavasoli a, Ahmad Reza Mohamadnia c, Alfredo Cravador d a Faculdade de Ciências e Tecnologia (FCT), Universidade do Algarve, Campus de Gambelas, 8005-139 Faro, Portugal b Department of Biochemistry, Faculty of Veterinary Medicine, Shiraz University, Shiraz 71345, Iran c Department of Clinical Sciences, School of Veterinary Medicine, Shahrekord University, 115 Shahrekord, Iran d IBB/CGB-Universidade do Algarve, Campus de Gambelas, 8005-139 FARO, Portugal article info abstract Article history: The scope of this study was to identify sequence polymorphisms in the β-1,4- Received 10 November 2009 galactosyltransferase-I gene (B4GALT1), the gene which encodes the catalytic part of lactose Received in revised form 25 March 2010 synthase enzyme. -
The Dimeric Structure of Wild-Type Human Glycosyltransferase B4galt1
RESEARCH ARTICLE The dimeric structure of wild-type human glycosyltransferase B4GalT1 ¤ Deborah Harrus, Fawzi Khoder-AghaID, Miika Peltoniemi, Antti Hassinen , Lloyd Ruddock, Sakari Kellokumpu, Tuomo GlumoffID* Faculty of Biochemistry and Molecular Medicine, University of Oulu, Aapistie 7A, Oulu, Finland ¤ Current address: Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland * [email protected] a1111111111 a1111111111 a1111111111 Abstract a1111111111 a1111111111 Most glycosyltransferases, including B4GalT1 (EC 2.4.1.38), are known to assemble into enzyme homomers and functionally relevant heteromers in vivo. However, it remains unclear why and how these enzymes interact at the molecular/atomic level. Here, we solved the crystal structure of the wild-type human B4GalT1 homodimer. We also show that B4GalT1 exists in a dynamic equilibrium between monomer and dimer, since a purified OPEN ACCESS monomer reappears as a mixture of both and as we obtained crystal forms of the monomer Citation: Harrus D, Khoder-Agha F, Peltoniemi M, and dimer assemblies in the same crystallization conditions. These two crystal forms Hassinen A, Ruddock L, Kellokumpu S, et al. (2018) The dimeric structure of wild-type human revealed the unliganded B4GalT1 in both the open and the closed conformation of the Trp glycosyltransferase B4GalT1. PLoS ONE 13(10): loop and the lid regions, responsible for donor and acceptor substrate binding, respectively. e0205571. https://doi.org/10.1371/journal. The present structures also show the lid region in full in an open conformation, as well as a pone.0205571 new conformation for the GlcNAc acceptor loop (residues 272±288). The physiological rele- Editor: Isabelle AndreÂ, University of Toulouse - vance of the homodimer in the crystal was validated by targeted mutagenesis studies cou- Laboratoire d'IngeÂnierie des Systèmes Biologiques et des ProceÂdeÂs, FRANCE pled with FRET assays. -
1716988115.Full.Pdf
Human N-acetylglucosaminyltransferase II substrate recognition uses a modular architecture that includes a convergent exosite Renuka Kadirvelraja,1, Jeong-Yeh Yangb,1, Justin H. Sandersa, Lin Liub, Annapoorani Ramiahb, Pradeep Kumar Prabhakarb, Geert-Jan Boonsb, Zachary A. Wooda,2, and Kelley W. Moremena,b,2 aDepartment of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602; and bComplex Carbohydrate Research Center, University of Georgia, Athens, GA 30602-4712 Edited by Karen Colley, University of Illinois College of Medicine, Chicago, IL, and accepted by Editorial Board Member Gregory A. Petsko March 23, 2018 (received for review September 28, 2017) Asn-linked oligosaccharides are extensively modified during tran- trimming, and extension reactions in the lumen of the Golgi complex sit through the secretory pathway, first by trimming of the to generate the multibranched, complex-type glycans found on cell- nascent glycan chains and subsequently by initiating and extend- surface and secreted glycoproteins (2) (Fig. 1). The enzymatic steps ing multiple oligosaccharide branches from the trimannosyl glycan required for the synthesis of these complex-type structures follow a core. Trimming and branching pathway steps are highly ordered discrete hierarchy based on the substrate specificities of the re- and hierarchal based on the precise substrate specificities of the spective enzymes. However, little is known regarding the structural individual biosynthetic enzymes. A key committed step in the basis for this substrate specificity. The first step in the glycan β synthesis of complex-type glycans is catalyzed by N-acetylglucosa- branching pathway is the addition of a 1,2GlcNAc to the core α N minyltransferase II (MGAT2), an enzyme that generates the second 1,3Man residue by -acetylglucosaminyltransferase I (MGAT1) to GlcNAcβ1,2- branch from the trimannosyl glycan core using UDP- produce the GlcNAcMan5GlcNAc2-Asn intermediate (4).